Course COBREXA

Section outline

• Select section COBREXA.jl

  Collapse Expand

  COBREXA.jl

  Collapse all Expand all

  
  

  • Select activity Welcome to COBREXA course! Here you can find many ...

    

    Welcome to COBREXA course! Here you can find many useful links that will help you master the use of COBREXA.

    
    

  • Select activity A metabolic modeling at scale.COBREXA.jl is a pack...

    A metabolic modeling at scale.
    

    
    COBREXA.jl is a package for COnstraint Based Reconstruction and EXascale Analysis, designed for researchers interested in metabolic modeling. Using constrained models, COBREXA includes algorithms such as finding optimal balanced fluxes involved in metabolism, and discovering the limits of known metabolic networks. As a distinctive feature, COBREXA.jl is highly parallelizable, allowing users to employ high-performance computing resources to speed up their analysis. The design allows it to scale to exascale supercomputer systems, which can perform as many as 10^18 floating point operations per second.
    
    
• Select section Tool repositories

  Collapse Expand

  Tool repositories

  A link to tool repository / repositories
  

  • Select activity COBREXA repositories

    

    COBREXA repositories URL
  • Select activity COBREXA on bio.tools

    

    COBREXA on bio.tools URL
• Select section Tools platforms/specifics

  Collapse Expand

  Tools platforms/specifics

  • Select activity see https://github.com/LCSB-BioCore/COBREXA.jlAny ...

    • see https://github.com/LCSB-BioCore/COBREXA.jl
    • Any OS supported by Julia, see https://julialang.org/downloads/
    • https://github.com/LCSB-BioCore/COBREXA.jl
      
• Select section Prior Knowledge needed for this tool:

  Collapse Expand

  Prior Knowledge needed for this tool:

  • Select activity Running COBREXA.jl requires basic knowledge of wri...

    Running COBREXA.jl requires basic knowledge of writing scripts. Algorithms model metabolic pathways, requiring some understanding of the underlying biological processes and terminology. A rich source of examples is available to get you started.
    
    To learn the terminology about metabolic models: https://www.nature.com/articles/nbt.1614
    
    Accelerating the analysis:
    For accelerating the analysis using high-performance computing, users should have basic familiarity with working in the command line, and have access to a supercomputing environment.
    
    You can learn about the command line with the following tutorials:
    https://ubuntu.com/tutorials/command-line-for-beginners#1-overview
    https://tutorial.djangogirls.org/en/intro_to_command_line/
    
    To learn about Slurm (job scheduler): https://researchit.las.iastate.edu/slurm-basics
    

  • Select activity Command line (mac, linux, windows) 1

    

    Command line (mac, linux, windows) 1 URL
  • Select activity Command line (mac, linux, windows) 2

    

    Command line (mac, linux, windows) 2 URL
  • Select activity julia programing language

    

    julia programing language URL
  • Select activity Recommended: basics of Slurm or some other job submission system

    

    Recommended: basics of Slurm or some other job submission system URL
  • Select activity A brief overview of the "most basic" analysis

    

    A brief overview of the "most basic" analysis URL
• Select section Work with COBREXA

  Collapse Expand

  Work with COBREXA

  • Select activity To start using COBREXA.jl, follow the simple examp...

    To start using COBREXA.jl, follow the simple examples on the COBREXA.jl page

    
    

• Select section Tutorials & resources:

  Collapse Expand

  Tutorials & resources:

  Here you can find our recommended tutorials and resources for COBREXA.
  

  • Select activity Documentation and tutorials

    

    Documentation and tutorials URL

    includes: reference, 4 basic tutorials (a good training material), 2 advanced tutorials, many notebooks (good as a copypaste resource)
  • Select activity Training material

    

    Training material URL
  • Select activity Distributed processing tutorial

    

    Distributed processing tutorial URL
  • Select activity COBREXA.jl: Metabolic Modeling on HPC

    COBREXA.jl: Metabolic Modeling on HPC

    
    
  • Select activity Analysis of huge metabolic models with COBREXA.jl ...

    Analysis of huge metabolic models with COBREXA.jl

    
    
  • Select activity Oznaka